Contacts of the helix formed by residues 536 - 540 (chain B) in PDB entry 3V9G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 536 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.6 25.4 - - + +
183A GLN* 3.3 32.0 + - + -
197A TYR* 3.7 20.9 + + - -
536A HIS* 5.8 2.7 - + - -
539A LEU* 3.7 33.2 - - + +
544A PRO* 5.6 4.8 - - - +
530B ASP 4.6 3.4 - - - +
531B LYS* 6.1 2.5 - - + -
534B GLY 3.3 1.0 - - - -
535B PRO* 1.3 95.6 - - + +
537B TYR* 1.3 67.6 + - - +
538B ILE 3.3 2.5 - - - -
539B LEU* 3.0 27.7 + - + +
540B ARG* 4.2 2.9 + - - +
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Residues in contact with TYR 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASN* 4.6 10.8 - - - +
218B ASN* 3.5 25.0 + - - -
219B LEU* 4.1 5.7 - - - +
222B ALA* 3.6 25.6 - - + -
283B ASN* 3.0 34.8 + - - -
312B ALA* 5.4 2.7 - - + -
530B ASP* 3.6 30.0 + - + -
531B LYS* 3.6 16.0 + - - +
532B PRO* 3.6 36.1 - - + +
533B GLY 4.8 0.7 - - - +
534B GLY 3.7 8.4 + - - +
535B PRO 3.6 1.0 - - - -
536B HIS* 1.3 77.4 - - - +
538B ILE* 1.3 66.1 + - + +
539B LEU 3.0 1.4 + - - -
540B ARG* 3.1 22.0 + - + +
541B TRP* 3.8 17.1 - + - -
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Residues in contact with ILE 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASN* 3.9 35.9 - - + +
176B TYR* 3.6 17.0 - - + +
177B ALA* 3.6 33.0 - - - +
180B LEU* 4.2 11.2 - - + -
222B ALA* 4.8 5.4 - - + -
225B LEU* 4.8 2.5 - - + -
226B MET* 3.9 32.9 - - + +
534B GLY 5.0 0.2 + - - -
535B PRO 3.8 17.0 - - - +
537B TYR* 1.3 78.5 - - + +
539B LEU* 1.3 62.3 + - + +
541B TRP* 2.8 33.9 + - - +
542B THR* 3.7 4.7 + - - +
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Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A HIS* 3.8 28.7 - - + +
539A LEU* 3.3 34.1 - - + -
180B LEU* 3.8 38.4 - - + -
197B TYR* 5.2 1.1 - - + -
310B ARG* 3.5 3.5 + - - -
535B PRO 4.9 2.0 - - - +
536B HIS* 3.0 25.5 + - + +
537B TYR 3.0 0.8 + - - -
538B ILE* 1.3 80.8 - - + +
540B ARG* 1.3 65.3 + - + +
541B TRP 3.0 1.0 + - - -
542B THR* 3.4 27.5 + - + +
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Residues in contact with ARG 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A ASP* 4.6 5.3 + - - -
540A ARG* 3.9 45.1 - - - +
200B LEU* 4.1 0.7 - - - +
310B ARG* 2.8 82.5 + - + +
311B LEU 4.8 9.7 + - - +
312B ALA* 5.6 3.1 - - + +
530B ASP* 3.7 39.4 + - + +
536B HIS 5.0 2.5 - - - +
537B TYR* 3.1 15.7 + - + +
539B LEU* 1.3 79.2 + - - +
541B TRP* 1.3 80.4 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il